Copper wire has a nasty tendency to cause bubbles, when the gas from the hot metal escapes.

I haven't tried it personally, but I've been advised to place small chips of clear frit at the edges, between the clear top layer and the layers beneath. This way, when the layers fuse, the centre will fall first and the resulting gasses will be forced to the edges, thereby escaping the piece altogether - hopefully - and getting rid of the bubbles.

I do a lot of pieces with frit and scrap glass, so I get bubbles all the time! As long as they're a) not too near the surface and b) non-gargantuan, I tend to think of them as 'design features'... ;-)

And if they really bug you - drilling through the bubble with a Dremel/diamond drill bit and then refusing normally results in much smaller bubbles or a complete absence of them. It would certainly be more cost effective - not to say less heartbreaking too - than throwing away the ones you think are too 'bubbly'.